feat: Phantom atoms #1953
Merged
feat: Phantom atoms #1953
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
trisyoungs
force-pushed
the
phantom-atoms
branch
from
314fdbe
to
36b734a
Compare
…ndices for NeutronSQ.
trisyoungs
force-pushed
the
phantom-atoms
branch
from
36b734a
to
e76602a
Compare
rprospero
approved these changes
Oct 14, 2024
Comment on lines
+169
to
+198
| dissolve::for_each_pair(ParallelPolicies::seq, speciesAtomTypes.begin(), speciesAtomTypes.end(), | ||
| [&](int spTypeI, const AtomTypeData &atd1, int spTypeJ, const AtomTypeData &atd2) | ||
| { | ||
| // First, check that both of atom types used in the species are present in the weights | ||
| // atomTypes_. They may legitimately not be if, for example, they are phantom atoms. | ||
| auto optPairIndex = atomTypes_.indexOf(atd1.atomType(), atd2.atomType()); | ||
| if (!optPairIndex) | ||
| return; | ||
| auto &[typeI, typeJ] = *optPairIndex; | ||
|
|
||
| auto &localI = atomTypes_[typeI]; | ||
| auto &localJ = atomTypes_[typeJ]; | ||
|
|
||
| // If an AtomType is exchangeable, add the averaged scattering length from the local | ||
| // AtomTypesList instead of its actual isotopic length. | ||
| bi = localI.exchangeable() | ||
| ? bi = localI.boundCoherent() | ||
| : Sears91::boundCoherent(tope->atomTypeIsotope(atd1.atomType())); | ||
| bj = localJ.exchangeable() | ||
| ? localJ.boundCoherent() | ||
| : Sears91::boundCoherent(tope->atomTypeIsotope(atd2.atomType())); | ||
|
|
||
| // Convert from fm to barns | ||
| bi *= 0.1; | ||
| bj *= 0.1; | ||
|
|
||
| intramolecularWeights_[{typeI, typeJ}] += weight * bi * bj; | ||
| intraNorm[{typeI, typeJ}] += weight; | ||
| globalFlag[{typeI, typeJ}] = true; | ||
| }); |
There was a problem hiding this comment.
There's a way to do all of this in parallel with the PairIterator and std::transform_reduce, but it's probably not worth the trouble unless this is a serious bottleneck.
There was a problem hiding this comment.
Shouldn't be as it's called once per module per iteration, so I'm inclined to leave it as-is.
Comment on lines
+45
to
+47
| Phantom = -1, | ||
| Physical, | ||
| Any |
There was a problem hiding this comment.
A possible suggestion here would be to assign Any the value of zero. The could change a bunch of conditionals from
if (presence == SpeciesAtom::Presence::Any)
to merely being
if (presence)
There was a problem hiding this comment.
For clarity (and my own sanity when I look back at this in six months and don't understand what I've written) I think we should keep the explicit comparison and enum as they are.
Co-authored-by: Adam Washington <adam.washington@stfc.ac.uk>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR completes #1900 although the final product is to introduce "phantom" rather than "artificial" atoms.
Briefy, a phantom atom is a normal
SpeciesAtomand is part of aSpecies, connected to otherSpeciesAtoms, and is evolved by MC / MD in the standard way. However, it makes no contribution to correlation functions or weights as calculated by the various correlation modules. Thus, they can affect the behaviour of a species / system but are invisible to structural probes.Closes #1900.
Follow-on issue #1952 captures further work.